[AMBER] TI simulations

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 30 Apr 2020 19:09:58 +0000

I came across a sample input file from Prof Kenneth Merzís group and it is an equilibration input file. These are the contents:
I have 3 queries:


What is the utility of setting ntwv =1 ? ( have never tinkered with this parameter in AMBER ever)
Also the same query about ntave=10 (What is the importance of ntave parameter)
If we do not mention press0=1, will it not be the default value. I thought ntp =1 means we are setting the pressure at 1 atm.

Thanks



NPT MD w/No position restraints and PME (sander)
&cntrl
  ntx = 5,
  irest = 1,
  ntpr = 1000,
  ntwx = 1000,
  ntwe = 1000,
  ntwr = 1000,
  ig = -1,

  ntf = 1,
  ntb = 2,
  ntp = 1, pres0 = 1.0, taup = 2.0,gamma_ln = 2.0,
  cut = 9.0,
  iwrap = 1,
  nsnb = 10,

  nstlim = 1000000,
  t = 0.0,
  nscm = 1000,
  dt = 0.001,

  temp0 = 300.0,
  tempi = 300.0,
  ntt = 3,
  tautp = 2.0,

  ntc = 1,
  iwrap=1, ioutfm=1, ntwv=-1,ntave=1000,
  icfe = 1, ifsc = 1,
  timask1=':1',
  timask2=':2',
  scmask1=':1.CB,HB1,HB2,HB3,',
  scmask2=':2.CK1,CK2,NK1,CK3,NK2,CK4,HK1,HK2,HK3,',
  clambda=0.5,
&end
&ewald
   skinnb=2, nfft1=96, nfft2=96, nfft3=96,
/



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Received on Thu Apr 30 2020 - 12:30:01 PDT
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